added suppress_md5 option to these workflow functions

for consistency with the 'downstream' workflows
Returning choices as list and modifying alpha_diversity.py to use the new option type
udpated index headers to be read from a dict

rather than repeated many times through-out the code
Fixed issues 611 and 622.
Merge pull request #730 from gregcaporaso/issue-688

partially addresses #688
removed old output
added new output
Merge pull request #85 from josenavas/ampliconnoise

Adding test folder for the ampliconnoise.py script
Merge pull request #89 from gregcaporaso/issue-88

updated core diversity output
Change read mode for parameter files

Parameter files in these scripts were previously open without using the
'U' mode.

This should fix #727
Added support for empty distribution boxplots.

Support added at lower level distribution_plots.py code. Need to add tests and then work on make_distance_boxplots.py code to make sure that it will support empty distributions as well.
Updated existing distribution_plots.py tests.
Added tests for empty distributions and coloring.
Updated pairwise tests text to be clearer.
Fixes issue #711

Modifies the defaults as @gregcaporaso suggested so that if a depth is not passed it will use the deepest available. Updated the documentation in the script and library and added a test.
Fixed performance bug in make_otu_heatmap_html.py.

Also removed a lot of old commented-out code. Fixes #731.
Merge pull request #742 from jrrideout/issue_731

Fixed performance bug in make_otu_heatmap_html.py.
Merge pull request #736 from ElDeveloper/params_U

Change read mode for parameter files -- issue 727
Adding my name to credits
Updated to address initial problems.